A spy vessel is detected near Sand Island, launching reconnaissance UAVs, and the Wardog Squadron is ordered to intercept them and shoot them down but not damage the vessel itself. After shooting down the UAVs, the Wardog Squadron is attacked by unidentified fighters (MiG-21bis Fishbed, MiG-29A Fulcrum), and Bartlett orders weapons free, again in violation of Thunderhead's orders. Although Wardog is again victorious, the spy vessel unexpectedly fires a homing missile at Edge's F-5E Tiger II but hits Barlett´s F-4G Phantom II Wild Weasel instead and he is shot down. Barlett successfully bails out in the water and Wardog is recalled back to base. A rescue helicopter is sent to pick Bartlett up but cannot locate him.

Yuktobania has declared war on Osea and launched a simultaneous surprise attack on the Osean Port St. Hewlett. Wardog Squadron is sent to assist the OFS Kestrel's VFA-206, led by Captain Marcus Snow in defending the port facilities and escaping vessels, including the Kestrel. Once the vessels make it out into open sea, Wardog is requested to destroy the blockade of Yuktobanian ships. The Kestrel makes it out safely.

The evening of the St. Hewlett raid, the Sand Island air base is attacked by Yuktobanian strategic bombers. Blaze, Nagase, and Chopper perform an emergency scramble and defend the island. In the middle of the air raid, another trainee, Hans Grimm, launches with Bartlett's spare plane to help Wardog. Lt.Col. Ford, who is supposed to replace the MIA Bartlett, attempts an emergency landing while the attack is still on-going but he is shot down and killed. As a result, Blaze is permanently promoted to Wardog Leader, while Grimm joins the squadron as Wardog Four.

The Wardog Squadron escorts OFS Kestrel and two other carriers from the Osean 3rd Naval Fleet, OFS Buzzard and OFS Vulture, as they relocate into the inland Bannion Sea. Shortly before the end of the mission, they are attacked by the Yuktobanian Air Force but fend them off. However, two burst missiles are then launched from the Yuktobanian submarine carrier Scinfaxi, which wipe out most of the VFA-206 and sink the Buzzard and Vulture. Wardog manages to climb to a safe altitude in time and survives, along with Captain Snow. With two carriers gone, Wardog is temporarily transferred to Heierlark Air Base for repairs and refueling and is tasked with escorting all available nuggets from Heierlark back to Sand Island with them.

Osea attempts to launch a laser module to be outfitted onto the Arkbird, a maneuverable orbiting spacecraft, in response to Yuktobania's use of the Scinfaxi. Yuktobania sends in airborne tanks, and eventually cruise missiles, to capture and destroy the base respectively. Wardog Squadron, in the area on their trip back to Sand Island, fend off the attack and the laser module is launched successfully.

Yuktobania recognizes the danger of the Sand Island base and launches a massive naval and aerial attack on it, reinforced by the Scinfaxi. The Wardog Squadron and the newly-arrived nuggets are sent to intercept. The Scinfaxi begins firing burst missiles, but the first three are vaporized by the Arkbird's new laser. The next ones, however, obliterate all of the nuggets before the Arkbird and the Wardog Squadron manage to sink the submarine, causing the fleet to fall back and give up the invasion.

Wardog Squadron is sent in pairs to patrol the northern coastline, out of the AA system near Akerson Hill. En route, Blaze and Nagase discover a damaged C-5 plane carrying Osean President Vincent Harling, who is on his way to North Point for top secret peace negotiations with the Yuktobanians. The Wardogs guide the C-5 through the AA system, then defend it against Yuktobanian fighters as it makes an emergency landing. The Osean 8492nd Squadron then secures the President, while Wardog returns to base.

The Osean Army prepares an amphibious landing operation on the Yuktobanian mainland near Bastok Peninsula. The peninsula is heavily fortified and the Wardog Squadron is called upon to provide close air support, as the Oseans capture the fortress, mainly to render the bunkers in the area useless with cooperation with the ground forces.

Following their defeat at Bastok Peninsula, the Yuktobanian forces are pulling back to their inland. Wardog Squadron is sent to intercept the escaping transport planes over Dresdene. Despite the enemy's use of E-767 jammers, Wardog successfully shot down all the transports. Simultaneously, however, the 8492nd Squadron launches a terrorist attack on a Yuktobanian engineering college near Wardog's area of operation, killing many civilians. The attack is blamed on the Wardog Squadron because the "8492nd Squadron" didn't officially exist in the Osean military.

This mission is played only if the player answered "Yes" to Chopper's question about the song "Face of the Coin" in mission 10.

In retaliation for the "Osean" terrorist attack in Dresdene, the Yuktobanians simultaneously launch an raid on the civilian Apito International Airport and chemical attack on Bana City. The Wardog Squadron, grounded in Oured for hearing, is sent to Apito while the Capital District Air Defense squadron is sent to Bana. After shooting down the enemy fighters, they have to deal with the Yuktobanian forces hidden in the transport planes (mistakenly marked as the Osean Air Force) that landed in the airport earlier. The enemies are destroyed in time and the civilian damage is minimized.

This mission is played only if the player answered "No" to Chopper's question about the song "Back of the Coin" in mission 10.

In retaliation for the "Osean" terrorist attack in Dresdene, the Yuktobanians simultaneously launch an raid on the civilian Apito International Airport and chemical attack on Bana City. The Wardog Squadron, grounded in Oured for hearing, is sent to Bana while the Capital District Air Defense squadron defends Apito. They receive four specialized Mirage 2000Ds armed with just the 30mm guns and loaded with neutralizing agent and proceed to neutralize the gas across the city. Afterwards, they assist the police in apprehending the terrorists by shooting down the helicopters they attempt to escape on.

This mission is played only if the player answered "Yes" to Chopper's question about the song "Face of the Coin" in mission 10.

To clear their name, the Wardog Squadron is sent to destroy a heavily defended, underground Yuktobanian munitions storage facility in Duga. Despite heavy resistance from commandos in the forest carrying shoulder-launched SAMs, Wardog manages to destroy most of the facility by detonating the munitions stored there and deals a severe blow to the Yuktobanian army supply chain.

This mission is played only if the player answered "No" to Chopper's question about the song "Back of the Coin" in mission 10.

To clear their name, the Wardog Squadron is sent to destroy a large Yuktobanian munitions factory in Sonza. Since the factory is protected by four defensive lines, each consisting of four radars, the Wardog splits up and destroys all radars in each line simultaneously to avoid detection. They then proceed to demolish the factory, dealing a severe blow to the Yuktobanian army supply chain.

A ballistic missile attack on the Osean ground forces leads Osean intelligence to discover a second Yuktobanian Scinfaxi-class submarine, called the Hrimfaxi. They send Wardog to destroy it as the Osean Army makes a decisive push for the Yuktobanian inland. Despite the lack of support from the Arkbird, Wardog manages to sink the submarine before it deals too much damage to the Osean Army. This feat earns them the fearful title of "Razgriz", a mythological demon after whom the site of their battle against Hrimfaxi was named.

The Wardog Squadron assists Sea Goblin in the extraction of Osean prisoners from the Yuktobanian POW camp in Glubina. After securing air superiority over the area, Wardog destroys the ground-based defenses firing at the Sea Goblin helicopter. Nagase, believing that Captain Bartlett may be among the inmates and distraught by feelings of guilt over him saving her earlier, is shot down when the operation is almost complete. She bails out, but the gunship sent immediately after her crashes because of the snow storm and she has to wait until the next morning for pickup.

The next morning, Blaze, Chopper, and Grimm lead the search-and-rescue mission for Nagase. They locate her distress beacon just before the Yuktobanian search parties find her, and escort an H-9 helicopter to her position while defending it from air and ground attack.

This mission is played only if the player answered "Yes" to Chopper's question about the song "Face of the Coin" in mission 15.

The Wardog Squadron escorts an Osean armored regiment and a bomber squadron as they attack a Yuktobanian field HQ and an air field, respectively, in the Jilachi Desert. Despite fierce aerial resistance, the HQ is destroyed and the airfield captured. Wardog then destroys Yuktobanian refueling planes and an AWACS that attempt to aid the local air force.

This mission is played only if the player answered "No" to Chopper's question about the song "Back of the Coin" in mission 15.

The Wardog Squadron escorts two Osean armored regiments as they simultaneously take over a Yuktobanian airfield and an oil refinery in the Jilachi Desert. The operation is successful, but then the Yuktobanians deploy a battleship to bombard the Osean forces from afar. The vessel is promptly sunk by Wardog.

The Wardog Squadron is given the honor of performing a ceremonial flyby over November City, where the Osean Vice President is to give an anti-war speech at the stadium. Although the speech turns out to be pro-war instead, the civilian audience starts singing an anti-war song. At this moment, Yuktobanian planes attack the city, and Wardog alone can hold them off while the civilians are being evacuated and reinforcements are scrambled. The reinforcements are then called off by the 8492nd Squadron, however, causing a confusion. Chopper's plane takes heavy damage from a missile hit, but because he waits until the civilians are evacuated from the stadium, his ejection seat malfunctions and he cannot bail out, crashing into the now-empty stadium. The rest of Wardog, audibly shaken by his death, holds off the enemy until the reinforcements finally arrive.

The Osean Army's assault on the Yuktobanian capital Cinigrad has been stalled by the impregnable Cruik Fortress for five days. With multiple heavy fire support bunkers, control towers, and an aircraft runway, the fortress has repelled two attempts to break through. Despite Wardog's weakened state, they are sent to provide close air support and guidance. Wardog engages in a battle with some aces in the Yuktobanian Air Force, and guides the armed forces through the fortress to completely pass right through, opening the way to the capital.

On their way back from Cruik Fortress, the Wardog rendezvous with an allied escort, which turns out to be the 8492nd Squadron. The 8492nd opens fire on Wardog, and the latter successfully escapes and races for Sand Island to report the incident.

Back on Sand Island, Wardog discovers that its vice commander Allen C. Hamilton is a traitor when he tries to kill them and, failing that, labels them and their mechanic Wolfgang Buchner as traitors instead. Blaze, Nagase, Grimm, Buchner, journalist Albert Gennette, and Chopper's dog Kirk escape Sand Island on four Hawk T.1s, pursued by the 8492nd. Buchner, revealed to be a former Belkan ace, leads the Wardog planes through a series of underground tunnels on a nearby island to shake off the pursuers. They eventually escape into the open sea and run into the OFS Kestrel's pilot Marcus Snow. Snow signals them to trust him and bail out, which they do. He then shoots down their planes and declares the Wardog dead, while Sea Goblin helicopters from the Kestrel secretly picks them up.

Wardog Squadron, now assisted by the Kestrel and Captain Snow, attempt to put the pieces together on what's been happening. With the help of the Andromeda, an intelligence ship in the Kestrel fleet which had intercepted a Belkan transmission, they located the location of President Harling in Belka. Wardog Squadron, Captain Snow, and Sea Goblin rescue Harling, and he brings Blaze, Nagase, Grimm, and Snow into his own personnel air squadron, named the Razgriz Squadron.

An encrypted transmission from an unknown source, picked up by the Andromeda, points toward a supposedly abandoned Belkan military facility at Mount Schirm. Blaze is sent there on a covert reconnaissance mission. Unarmed and solo, he flies through the dense early warning radar network, take two pictures of the Belkan planes bearing the markings of both Osea and Yuktobania, and escapes before they can catch up with him.

It is decided that the Belkan facility at Mt. Schirm, which was actually housing the nuclear weapons used in the last war, must be sealed for good to prevent any chance of nuclear weapons being smuggled out of it. Razgriz Squadron raids the facility and seals it by collapsing the mountain side it is dug into. Unbeknownst to them, however, the Belkans have already transported three nuclear bombs out of it.

Another encrypted message points towards Payavlenie Ravine in Yuktobania. There, the Razgriz Squadron discovers a Yuktobanian anti-war resistance cell, led by Alyosha, trying to dismantle one of the Belkan nuclear bombs. Alyosha requires the Razgriz to take out the Yuktobanian military searching for them. The situation is worsened by a Yuktobania's air defense system that limits the Razgriz to flying inside the canyon. After they destroy the enemy search parties, they are confronted by the Ofnir Squadron, the Yuktobanian counterpart to the Grabacr (who posed as the Osean 8492nd), and shoot them down. The nuke is successfully dismantled and sunk into the Ceres Ocean. En route, Alyosha forwards another message from their mysterious benefactor to the Razgriz, which hints that Captain Bartlett is still alive.

Another encrypted message, this time from Belka, informs the Kestrel crew that the Belkans are going to use the hijacked Arkbird to drop the other nuclear bomb they recovered onto the Yuktobanian city of Okchabursk. Razgriz is sent to shoot down the Arkbird the moment it descends for the drop-off. They are aided by an unknown Osean astronaut who sabotages the Arkbird before fleeing in an escape capsule, preventing the spaceship from ascending again. The Ghosts of Razgriz deal critical damage to the Arkbird, sinking it in the Ceres Ocean.

The mysterious benefactor who sent encrypted messages to the Kestrel is revealed to be Captain Bartlett, who escaped from imprisonment and joined the Yuktobanian resistance. This time, he needs the Razgriz to cover his escape from Yuktobania with the freed Prime Minister Nikanor. The squadron travels to the Pobeda Peninsula and clears the way for Bartlett, before confronting and shooting down the Grabacr Squadron.

A Yuktobanian fleet attacks the Kestrel and the Osean 3rd Naval Fleet in the Ceres Ocean. Nikanor manages to convince four Yuktobanian captains to join the Kestrel, but the rest open fire on the Kestrel, her fleet, and the defectors, sinking at least one of them. On Andersen's advice, the Prime Minister leaves for Oured to meet up with President Harling. The Razgriz Squadron launches to protect the Kestrel and their new allies, sinking first the attacking Yuktobanian fleet, then the Osean fleet that has been sent after the "renegade" carrier.

The data on the SOLG reveals that it will be used to launch the V2, a MIRV mass retaliation weapon that can obliterate half of either Osean or Yuktobanian cities. The Kestrel is sunk by a submarine attack but not before Razgriz takes off. The four planes make their way to Sudentor in Southern Belka, where the SOLG control center is hidden. Harling and Nikanor hold a peace press conference and many Osean and Yuktobanian units join Razgriz in Sudentor. After wiping out the defenses, the Razgriz Squadronflies into the huge tunnel where the SOLG controls are located, pursued by Hamilton. Simultaneously, Bartlett enters the tunnel from the other side to destroy the backup controls. They barely avoid collision inside but escape unharmed, while Hamilton is killed by a ricocheting enemy plane that came in after Bartlett.

It was then revealed that if the SOLG controls were ever cut off, the SOLG would automatically drop onto Oured itself, wiping out the entire city. The Ghosts of Razgriz are sent on their final mission to intercept and destroy the SOLG in the air. First, however, they have to defeat the Ofnir Squadron and the Grabacr Squadron escorting the station. Once they are defeated, the Razgriz Squadron destroys the SOLG core components, causing the entire station to blow up in the sky, its pieces falling harmlessly into the ocean.